Structure, Stability and Interaction Studies on Nucleotide Analogue Systems

Kolandaivel, P.; Kanakaraju, R.

doi:10.3390/i4080486

Cited by 6 publications

(7 citation statements)

References 21 publications

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“…For the sake of completeness, in Table we give all relevant bonded parameters. As can be seen in Table , the new parameter set predicts a dipole moment that closely matches the reference value and leads to an improved reproduction of experimental density of pure DMPH solution. Δ H vap is visibly smaller but still remains significantly larger than the reference value.…”

Section: Results and Discussionsupporting

confidence: 54%

“…While the calculated density of 100% (w/w) solution of DMPH compares well with experimental data, Δ H vap is over three times larger than the reference value. The value of the dipole moment of DMP – seems to be problematic as well, since the reference ab initio calculations at the MP2/6-31G* level of theory for isolated DMP – and DMP – interacting with up to three water molecules report dipole moments in the range from 4.6 to 7.1 D with the average value for eight alternative configurations equal to 6.0 D.…”

Section: Results and Discussionmentioning

confidence: 99%

“…813-78-5), the experimental liquid density was taken from and Δ H vap was predicted with ACD/Labs. The reference values of Δ G hyd and dipole moment for DMP – are from, respectively, Klauda et al and Kolandaivel and Kanakaraju . The dipole moment of DMP – was calculated with origin set as the ion’s center of mass.…”

Section: Results and Discussionmentioning

confidence: 99%

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Refined OPLS All-Atom Force Field Parameters for n-Pentadecane, Methyl Acetate, and Dimethyl Phosphate

2013

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OPLS All-Atom (OPLS/AA) is a generic all-atom force field which was fine-tuned to accurately reproduce condensed phase properties of organic liquids. Its application in modeling of lipid membranes is, however, limited mainly due to the inability to correctly describe phase behavior and organization of the hydrophobic core of the model lipid bilayers. Here we report new OPLS/AA parameters for n-pentadecane, methyl acetate, and dimethyl phosphate anion. For the new force field parameters, we show very good agreement between calculated and numerous reference data, including liquid density, enthalpy of vaporization, free energy of hydration, and selected transport properties. The new OPLS/AA parameters have been used in successful submicrosecond MD simulations of bilayers made of bacterial glycolipids whose results will be published elsewhere shortly.

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Section: Results and Discussionsupporting

confidence: 54%

Section: Results and Discussionmentioning

confidence: 99%

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Refined OPLS All-Atom Force Field Parameters for n-Pentadecane, Methyl Acetate, and Dimethyl Phosphate

2013

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“…Dimethyl phosphate anion (CH 3 -O) 2 -P(O) 2 represents the smallest realistic model containing the C-O-P-O-C phosphodiester linkage of the nucleic acid backbone and phospholipids. 37 Common notations used in spectroscopy suggest conformations with C-O-P-O(α.ζ) torsional angles of ~± 60 (deg.) as gauche (g), and those of ~180 (deg.)…”

Section: Resultsmentioning

confidence: 99%

Crystal Structure and Molecular Stereochemistry of Novel Polymeric Cu₂(DMP)₄₄(DMSO) as a Platform for Phosphate Diester Binding

Rafizadeh¹,

Tayebee²,

Amani³

et al. 2005

Bulletin of the Korean Chemical Society

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Treatment of a solution of CuCl 2 in dimethyl phosphate (DMP) with DMSO under nitrogen atmosphere afforded to a light blue fluorescence powder. Slow evaporation of H 2 O-DMSO solution of this powder resulted in blue-sky crystals of a new polymeric Cu(II) complex, with a unit cell composed of Cu 2 (DMP) 4 (DMSO), (1). The crystal and molecular structure of the complex acquired crystallographically. Compound (1) crystallizes in the monoclinic space group P2 1 /n with a = 12.8920(11) Å, b = 13.1966(11) Å, c = 14.7926(13) Å, α = 90 o , β = 98.943(2) o , γ = 90 o , V= 2486.1(4) Å 3 , and Z = 4. A square pyramidal environment for the metal center was established by coordination of oxygen atoms of four bridging DMP ligands in the basal positions and binding a tri-centered oxygen atom of DMSO in the apical disposition of Cu(II). The sixth position was also affected by a weak interaction with the sulfur atom of another DMSO. The phosphorous atom in the bridging DMP was arranged in a deformed tetrahedron with (gg) conformation for methyl esters with C 2v symmetry.

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“…Dimethyl phosphate anion (CH 3 -O) 2 -P(O) 2 represents the smallest realistic model containing the C-O-P-O-C phosphodiester linkage of the nucleic acid backbone and phospholipids [40]. For description of the different phosphate conformations we adopt notation commonly used in spectroscopy.…”

Section: Introductionmentioning

confidence: 99%

Crystal structure and molecular stereochemistry of polymeric Cu2(DMP)4(DMSO) as a platform for phosphate diester binding

Rafizadeh¹,

Tayebee²,

Amani³

et al. 2006

Cryst. Res. Technol.

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Treatment of a solution of CuCl 2 in dimethyl phosphate (DMP) in an inert solvent under nitrogen atmosphere resulted in a light blue fluorescence powder. Slow evaporation of H 2 O-DMSO solution of this powder led to the formation of blue-sky crystals of a new polymeric Cu(II) complex, with a unit cell composed of Cu 2 (DMP) 4 (DMSO), (1). The crystal and molecular structure of the complex was established crystallographically. Compound (1) crystallizes in the monoclinic space group P2 1 /n with a = 12.8920(11)Å, b = 13.1966(11)Å, c = 14.7926(13)Å, α = 90°, β = 98.943(2)°, γ = 90° and Z = 4. A square pyramidal environment for the metal center is established by coordination of oxygen atoms of four bridging DMP ligands in the basal positions and a tri-centered oxygen atom of DMSO in the apical disposition. The sixth position is also affected by a weak interaction with the sulfur atom of DMSO. The phosphorous atom in the bridging DMP is arranged in a deformed tetrahedron with gg conformation for methyl esters with C 2v symmetry. Accordingly, the angles of methoxy substituents are unexpectedly smaller than the bridging oxygens, and synchronous z-in and z-out distortions are suggested for DMP anion. The oxygen atom of SOCuCu´ fragment derived from DMSO, functions as a tri-centered nuclei lie almost in a trigonal triangle environment. This study helps provide further insights into the binding nature of phosphate esters to the active sites of enzymes, which catalyze phosphoryl transfer reactions.

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Structure, Stability and Interaction Studies on Nucleotide Analogue Systems

Cited by 6 publications

References 21 publications

Refined OPLS All-Atom Force Field Parameters for n-Pentadecane, Methyl Acetate, and Dimethyl Phosphate

Refined OPLS All-Atom Force Field Parameters for n-Pentadecane, Methyl Acetate, and Dimethyl Phosphate

Crystal Structure and Molecular Stereochemistry of Novel Polymeric Cu₂(DMP)₄₄(DMSO) as a Platform for Phosphate Diester Binding

Crystal structure and molecular stereochemistry of polymeric Cu2(DMP)4(DMSO) as a platform for phosphate diester binding

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Structure, Stability and Interaction Studies on Nucleotide Analogue Systems

Cited by 6 publications

References 21 publications

Refined OPLS All-Atom Force Field Parameters for n-Pentadecane, Methyl Acetate, and Dimethyl Phosphate

Refined OPLS All-Atom Force Field Parameters for n-Pentadecane, Methyl Acetate, and Dimethyl Phosphate

Crystal Structure and Molecular Stereochemistry of Novel Polymeric Cu2(DMP)44(DMSO) as a Platform for Phosphate Diester Binding

Crystal structure and molecular stereochemistry of polymeric Cu2(DMP)4(DMSO) as a platform for phosphate diester binding

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Crystal Structure and Molecular Stereochemistry of Novel Polymeric Cu₂(DMP)₄₄(DMSO) as a Platform for Phosphate Diester Binding